Aim
Sequencing technology has replaced conventional
Conclusion
This study shows that whole genome sequencing approach for Shigella O-antigen analysis has greater discriminative power than other methods using different bioinformatics pipeline for identification of nonserotypeable Shigella.
Methods
Genome sequences were analyzed using online tools based on 16S rRNA, k-mer, gyrB sequences and analysis of O-antigen arrangement was done using PATRIC database for species identification. Sequence types, plasmid types, antimicrobial resistance and virulence genes were also investigated.
Results
The SpeciesFinder using 16S rRNA sequences identified only 74% of the isolates, whereas KmerFinder and gyrB sequence analysis identified 100% of the isolates to its species level. Antimicrobial resistance, virulence and plasmid incompatibility groups were identified in all the isolates. Sequence types were determined.